simulation_name	        water.6.1m     		! output files will carry this name + their specific extension
ensemble_type	 	0			! 0: NVE, 1: NVT, 2: anisotropic NPT, 3: semi-isotropic NPT, 4: isotropic NPT
nsteps			1000000       	! number of simulation steps
dt			0.1	    	   	! time step in fs

reposition_atoms	0			! 0: just fit to periodic boundaries, 1: CoM to the center of box, 3: CoM to the origin
restrict_bonds 		0			! enforce the bonds given in CONECT lines of pdb file for this many steps
tabulate_long_range	0			! denotes the granularity of long range tabulation, 0 means no tabulation
energy_update_freq 	1
remove_CoM_vel	        500			! remove the translational and rotational vel around the center of mass at every 'this many' steps

nbrhood_cutoff		5.0 	   		! near neighbors cutoff for bond calculations in A
bond_graph_cutoff	0.3			! bond strength cutoff for bond graphs
thb_cutoff		0.001	  		! cutoff value for three body interactions
hbond_cutoff		7.50			! cutoff distance for hydrogen bond interactions
q_err			1e-10		     	! relative residual norm threshold used in GMRES 

temp_init	      	0.0             	! desired initial temperature of the simulated system
temp_final 	      	300.0	        	! desired final temperature of the simulated system
t_mass		      	0.16666			! 0.16666 for Nose-Hoover nvt ! 100.0 for npt! in fs, thermal inertia parameter
t_mode                  0                       ! 0: T-coupling only, 1: step-wise, 2: constant slope
t_rate                 -100.0                   ! in K
t_freq                  4.0                     ! in ps

pressure 		0.000101325	       	! desired pressure of the simulated system in GPa, 1atm = 0.000101325 GPa
p_mass		        5000.00        		! in fs, pressure inertia parameter
compress 		0.008134     		! in ps^2 * A / amu ( 4.5X10^(-5) bar^(-1) )
press_mode		0			! 0: internal + external pressure, 1: ext only, 2: int only

geo_format		1			! 0: xyz, 1: pdb, 2: bgf
write_freq		10000  			! write trajectory after so many steps
traj_compress		0			! 0: no compression  1: uses zlib to compress trajectory output
traj_format		0			! 0: our own format (below options apply to this only), 1: xyz, 2: bgf, 3: pdb
traj_title		SILICA_NVT		! (no white spaces)
atom_info		1			! 0: no atom info, 1: print basic atom info in the trajectory file
atom_forces		0			! 0: basic atom format, 1: print force on each atom in the trajectory file
atom_velocities		0			! 0: basic atom format, 1: print the velocity of each atom in the trajectory file
bond_info		1			! 0: do not print bonds, 1: print bonds in the trajectory file
angle_info		1			! 0: do not print angles, 1: print angles in the trajectory file 
test_forces		0			! 0: normal run, 1: at every timestep print each force type into a different file

molec_anal		0			! 1: outputs newly formed molecules as the simulation progresses
freq_molec_anal		0			! perform molecular analysis at every 'this many' timesteps
dipole_anal		0			! 1: calculate a electric dipole moment of the system
freq_dipole_anal	1			! calculate electric dipole moment at every 'this many' steps
diffusion_coef		0			! 1: calculate diffusion coefficient of the system
freq_diffusion_coef	1			! calculate diffusion coefficient at every 'this many' steps
restrict_type		2			! -1: all types of atoms, 0 and up: only this type of atoms
